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Samantha Cross received her PhD in Paleontology Linguistics from Harvard almost a year before the events of Nightfall. She turned down a seven figure contract with the NSA and instead decided to "dig holes in the jungle". In an interview, she revealed that she was born with a rare neurological condition, which allowed her brain to process complex patterns into a code or language. Because of this condition, she was known as a natural code breaker. Because of her publicity, Cross was brought out to the Nightfall Program's head facility in Alaska by David Archer to study the Cryptid specimens he retrieved from Colorado.

Cross had spent months at the Nightfall facility learning about the Cryptid species. During her time there, Archer and the other members of the project denied her questions she wanted answers to. After four months of learning the origins of Cryptids, Archer tasked her with the decoding of the Ark, an obsidian stone carved with Cryptid glyphs found at the Colorado colony. After weeks of insomnia caused by her devotion to decode the obelisk, Archer unveiled his newest creation, the monstrous Breeder, causing Samantha to fear the true intentions of Nightfall. Giving into her suspicions, she breached the facility's location to the U.S. government, begging them to put an end to the group's work. Unbeknownst to Cross, her ongoing translations of the Ark began affecting her subconscious, making her suffer from the mimetic virus the stone carried, allowing her to broadcast the telepathic commands sent to the Cryptids from their distant commanding Ancestors. Under their influence, Cross breached Nightfall's hatchery in an outbreak that slaughtered 127 of the Program's employees, her being one of the remaining survivors due to the Cryptids' refusal to harm her.

The U.S. Military organized a Rapid Reaction Force codenamed CIF Team One to retrieve Dr. Cross, gather intelligence related to the Nightfall project, under the command of DIA's General Castle. After encountering and defeating the Breeder for the first time, Castle declared Cross among the casualities; however, Samantha revealed over the intercom she was hiding in the facility's research lab.

After breaching the lab, Cross prepared to kill herself after finally finishing the translations of the Ark, her brain slowly defecting further to the Cryptid enemy. Moments later, Archer quickly incapacitated and kidnapped Cross, escaping from the compound and leaving CIF Team One at the mercy of the Breeder. As the military cleaned up the second outbreak, an unconscious Cross was taken aboard Stormbreaker, Archer's escape vessel, and oversaw the bonding of her brain to the Beacon Amplifier, a device designed by surviving Nightfall scientist Dr. Kassar, to lead Archer and his men to the next Ark.

Days into the voyage, Archer learned of Cross' telepathic communication with the Cryptids, believing her to be the key to taking control of the creatures. To investigate this clairvoyant, Dr. Kassar was instructed to begin a series of psychological evaluations on Cross, her mind now completely deteriorated to the Cryptid masters, making Kassar fearful the virus turned her to something more than human. Throughout the psychological evaluations, Cross continually warned Kassar about his impending doom, and made Kassar question about who Cross was siding with: the human race, or the Cryptid race. As well, Kassar questions Samantha's physical state, as her brain would have practically liquefied from what his diagrams indicated, which should have caused her to die. Samantha's presence caused Stormbreaker's crew to experience vivid and terrifying nightmares, spreading rumors of mutiny and even one crew member attempting to kill Cross in her sleep. Enraged, Archer fed the man to Cryptid larvae, intending on beheading Cross when the time was right to wield her brain as a sabotage weapon against the Cryptid commanders. The next time Dr. Kassar did a psychological evaluation on her, Cross mentioned the existence of a guardian, who was designed to eliminate anyone who tried to infiltrate and discover the Arks. She then orders the Cryptids to kill Kassar.

Over three weeks after the Nightfall outbreak, Cross used her telepathy to summon the Kraken, the protector of the Arks as the vessel reached the shores of Ball's Pyramid, the location of the second Ark, as well as a third outbreak of the Cryptid specimens aboard the ship. Responding to a mayday broadcast, General Castle dispatched CIF Team One to pacify the outbreak and rescue Archer as a double-agent, as per their earlier agreements to gain his help in the Cryptid war under the condition Cross' head is brought out from the vessel. Protected by a shield of bulletproof glass, the Beacon room was flooded with chlorine gas that would poison Cross, allowing for the safe removal of her head. However, upon reaching lethality, she disappeared from the ship entirely, the Beacon Amplifier along with her. Castle and his men searched for Cross amid the wreckage of Stormbreaker, later declaring her amongst the deceased from the sinking of the vessel. Shortly after her disappearance, the military descended upon Ball's Pyramid, locating a Cryptid master in the process. Little did they know that an ambush was ordered upon their arrival to the Ark.

Unbeknownst to anyone, Cross had survived the Stormbreaker's destruction and was telepathically summoned to Ball's Pyramid by the Ancestors. Inside the Ark, she foresaw the Ancestors' intentions: to awaken all of the Arks and release the Cryptids onto the Earth's surface, eliminating the human race. After Archer and his squad arrived in Ball's Pyramid, she walks up to Archer and dismembers his infected right arm; she then proposes a deal to Archer: she will guide him and his soldiers into the Ark for the brain of an Ancestor, and in return she would have a passage off of the island, which Archer accepts. Once Archer received what he needed, however, he attempted to shoot Cross, in order to retrieve her head, completing his desire of using her head as "the ultimate weapon" against the Cryptids, akin to how Perseus utilized Medusa's decapitated head as a weapon in Greek mythology. Samantha responded by seizing control of Archer's free arm, forcing him to kill his men and shoot himself in the leg, severely wounding Archer in the process. Cross left him to die, and managed to reach the surface of Ball's Pyramid, allowing Arclight to rescue her along with CIF Team 1.

With both CIF Team 1 and Cross aboard, Arclight left the island and headed to the Exodus launch site. While en route to their destination, General Castle contacted the pilot of the osprey and orders them to protect the Cortex, as he didn't know if they could trust Cross. Meanwhile, the Ancestors attempted to regain their asset, influencing Cross to steal the Cortex. As Samantha reached down to grab it, the co-pilot quickly raises his pistol and points it to her head, attempting to execute her for attempted theft of the Cortex. She cryptically warns him to "fasten his seat belt", shortly before a Gargoyle smashes through the cockpit, killing the pilots and causing the osprey to crash, allowing her to once more vanish and leave the CIF Team stranded.

Three months later, Cross returned once more to help the CIF Team and Castle, explaining she had the Cortex and planned to save mankind from extinction. After placing the Cortex in the Medusa weapon, Cross told the team that she would be getting on the shuttle, but the operatives would not, as they were in need to activate the Medusa when it was fully charged in order to clear the area for a safe launch. She boards the shuttle and, along with the crew on board, managed to reach the space station. Cross, once aboard Exodus, seats herself in a replica Beacon Amplifier and acknowledges that she will use her powers to help make a difference between survival and extinction. As she was inside the amplifier, her eyes turned from hazel, to red.